Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Differential analysis for high density tiling microarray data.

  PMID 17892592 · PMC2231405 · BMC bioinformatics · 2007 · 8 claims · 6 setups

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  gSAM, a generalized extension of Significance Analysis of Microarrays (SAM), uses a piece-wise function to segment genome-wide differential response by protein-coding vs non-coding regions and by 5' vs 3' vs intra-genic bias within genes, rather than treating a gene as an atomic unit.

  hl60 profiling chip-on-chip

• DeepRNA-Reg: a deep-learning based approach for comparative analysis of CLIP experiments.

  PMID 41055236 · PMC12505516 · RNA biology · 2025 · 8 claims · 5 setups

  Has reproduction · 100

  DeepRNA-Reg, a recurrent neural network-based algorithm, provides a superior prediction set for differential HITS-CLIP analysis compared to dCLIP.

  dgcr8 mir-23 predicted ago2 gene flow

• Epigenetics and chromatin structure regulate var2csa expression and the placental-binding phenotype in Plasmodium falciparum.

  PMID 41984626 · PMC13082790 · eLife · 2026 · 8 claims · 7 setups

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  var2csa transcriptional activation is associated with near-complete depletion of repressive H3K9me3 occupancy at the locus

  falciparum prbc nf54 scanning flow placental

• Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding.

  PMID 41639407 · PMC12900649 · Nature genetics · 2026 · 8 claims · 8 setups

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  Acute HDAC inhibition (TSA pulse) induces genome-wide H3K27 hyperacetylation and reorganizes the histone modification landscape, shifting more of the genome to an active state.

  e14 simulated mescs calibrated atac-seq bulk

• Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells.

  PMID 17267408 · PMC1865061 · Nucleic acids research · 2007 · 6 claims · 6 setups

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  Measuring allelic imbalance (AI) of two SNP alleles within the same sample is an effective approach for identifying cis-acting rSNPs, since each allele serves as an internal control for the other.

  tumor promoter hela cdna bead tag-microarray

• High-resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies.

  PMID 34010620 · PMC8096189 · Cell · 2021 · 8 claims · 5 setups

  Has reproduction · 87

  A Phage-DMS library tiling all single amino acid mutations across the SARS-CoV-2 spike ectodomain (plus D614G) was generated and validated with high sequence coverage.

  phage-displayed cloned plasma spike-pseudotyped phage-dms deep elisa

• OTX2 inhibits human pluripotent stem cell reprogramming toward 8-cell-like and morula-like states.

  PMID 41554740 · PMC12909843 · Nature communications · 2026 · 8 claims · 8 setups

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  OTX2 establishes a repressive barrier to the induction of 8CLCs from primed hPSCs

  tprx1-egfp otx2-ko primed preimplantation flow bulk single-cell

• Tissue proteomics reveals differential and compartment-specific expression of the homologs transgelin and transgelin-2 in lung adenocarcinoma and its stroma.

  PMID 19848416 · PMC2789179 · Journal of proteome research · 2009 · 6 claims · 6 setups

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  Transgelin (TAGLN), transgelin-2 (TAGLN2), and cyclophilin A (PPIA) are overexpressed in lung adenocarcinoma tissue compared to matched normal lung

  matched excised additional formalin-fixed 2-d lc-ms quantitative

• Prediction of condition-specific regulatory genes using machine learning.

  PMID 32329779 · PMC7293043 · Nucleic acids research · 2020 · 8 claims · 6 setups

  Has reproduction · 85

  ConSReg integrates expression, DAP-seq TF-DNA binding, and ATAC-seq open chromatin data into machine learning models to predict condition-specific regulatory genes

  arabidopsis zea bulk dap-seq atac-seq

• Machine learning and free energy clustering reveal PAH protein binding linked to AD risk.

  PMID 41953002 · PMC13053772 · iScience · 2026 · 8 claims · 8 setups

  Has reproduction · 78

  PARP1, PTPN1, and ITGA4 are core PAH protein targets identified via PPI network analysis and XGBoost feature selection from AD-associated DEGs

  brain geo predicted gse44771 wgcna differential protein-protein

• Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise.

  PMID 29335641 · PMC5864184 · The ISME journal · 2018 · 8 claims · 7 setups

  Has reproduction

  Increasing salinity to ≥43 ppt inhibits Trichodesmium growth while stimulating growth of the associated Alteromonas

  alteromonas trichodesmium differential classical smrt

• Cohesin regulates alternative splicing.

  PMID 36857449 · PMC9977177 · Science advances · 2023 · 7 claims · 8 setups

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  Cohesin regulates alternative splicing independently of its effects on transcription.

  hct116rmac hct116 recombinant hek293 bulk rt-pcr proximity

• Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.

  PMID 37138775 · PMC10149407 · iScience · 2023 · 8 claims · 7 setups

  Has reproduction · 100

  Hsp90-dependent gene expression varies among different yeast strains

  diverse same yeast genomes rna-seq v-src growth

• TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity.

  PMID 25391375 · PMC4315292 · Genome research · 2015 · 8 claims · 8 setups

  Has reproduction · 80

  TP53 binding events fall into three distinct categories defined by the local chromatin environment: TSS (H3K4me3+), enhancer (H3K4me1+/H3K4me3-), and distal (H3K4me1-/H3K4me3-) peaks.

  imr90 hct116 chip-seq rna-seq atac-seq

• Stemness genes and miR-1247-3p expression associate with clinicopathological parameters and prognosis in lung adenocarcinoma.

  PMID 37948380 · PMC10637681 · PloS one · 2023 · 8 claims · 8 setups

  Has reproduction · 90

  Stemness-related genes ORC1L, KIF20A, and DLGAP5 are upregulated in LUAD and correlate with altered immune cell infiltration (Th2, MDSC, HSC) and reduced patient survival.

  tcga gse40419 gse31210 gene bulk microarray univariate

• MicroRNA Enrichment and Docking-Based Evaluation of Ilomastat Targeting of MMP-2 in Esophageal Squamous Cell Carcinoma: Insights from a South African Cohort.

  PMID 42158110 · PMC13181172 · Computational and structural biotechnology journal · 2026 · 7 claims · 5 setups

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  The miR-29 family inhibits MMP-2 and represents a key regulatory axis in tumor invasion

  paired deg mmp-2 escc bulk pathway molecular

• Stage- and cluster-specific regulation of chondrogenic gene programs by Sox9 in mouse embryonic limb buds.

  PMID 41809054 · PMC12969044 · iScience · 2026 · 8 claims · 7 setups

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  scRNA-seq across five limb bud stages identifies four Sox9-high populations (chondroprogenitors 1, 2, 3, and mature chondrocytes) with distinct temporal dynamics

  forelimb scrna-seq cut&run embryo single-cell cut&run velocity

• OptiSyn: an interpretable, multi-omics-driven graph convolutional network framework for synergy-oriented drug combination design in disease treatment.

  PMID 41877167 · PMC13011277 · Chinese medicine · 2026 · 8 claims · 8 setups

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  Eight AS-associated hub genes were identified through integration of multi-omics datasets (DEG analysis, WGCNA, scRNA-seq, Mendelian randomization, PPI module analysis)

  gtex as-associated tcm representative differential weighted single-cell

• Mutational analysis of the preferential binding of human topoisomerase I to supercoiled DNA.

  PMID 19740104 · PMC3107988 · The FEBS journal · 2009 · 8 claims · 4 setups

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  Human topoisomerase I (topo70) does not dimerize either free in solution or when covalently bound to DNA, ruling out dimerization as the source of a second DNA binding site

  gst-topo70 topo70 32p-labeled 3h-labeled gst gel 32p-labeled

• Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation.

  PMID 29783948 · PMC5963079 · BMC genomics · 2018 · 8 claims · 8 setups

  Has reproduction · 85

  Whole transcriptome sequencing with extensive TSS mapping identified 3078 transcription start sites and 629 ncRNAs in V. cholerae N16961

  cholerae lexa identified directional end rt-pcr